[gmx-users] The structure property

[Chih-Ying Lin]

Hi
>From the following tutorial, the protein pdb file is downloaded from the
Protein Data Bank. Before running the MD simulation, we have to make sure
the structure property. I have some questions about this tutorials.

http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/

1. Make sure that there are NO Missing residues, missing atoms-
   http://www.rcsb.org/pdb/files/1lw9.pdb
    "Search for the presence of REMARK entries with numbers 465 and/or 470.
" => there are no REMARK 465 and REMARK 470  ???


2. The protonation state and side chain orientation of histidine residues
may be problematic. => How could I know if they are problematic? => How to
do the protonation process on the system?


3. From the tutorial => "Note the numbers of ions added, and verify that an
excess of 8 chloride ions is added for neutralization. Having replaced a
number of water molecules with ions, the system topology in 1LW9.top is not
correct anymore. Edit the topology file and decrease the number of solvent
molecules. Also add a line specifying the number of NA+ ions and a line
specifying the amount of CL-. "
 => Would you please explain this more?

Thank you very much

Lin
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